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Gene-oriented ortholog database: a functional comparison platform for orthologous loci

机译：面向基因的直系同源数据库：直系同源基因的功能比较平台

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The accumulation of complete genomic sequences enhances the need for functional annotation. Associating existing functional annotation of orthologs can speed up the annotation process and even examine the existing annotation. However, current protein sequence-based ortholog databases provide ambiguous and incomplete orthology in eukaryotes. It is because that isoforms, derived by alternative splicing (AS), often share higher sequence similarity to interfere the sequence-based identification. Gene-Oriented Ortholog Database (GOOD) employs genomic locations of transcripts to cluster AS-derived isoforms prior to ortholog delineation to eliminate the interference from AS. From the gene-oriented presentation, isoforms can be clearly associated to their genes to provide comprehensive ortholog information and further be discriminated from paralogs. Aside from, displaying clusters of isoforms between orthologous genes can present the evolution variation at the transcription level. Based on orthology, GOOD additionally comprises functional annotation from the Gene Ontology (GO) database. However, there exist redundant annotations, both parent and child terms assigned to the same gene, in the GO database. It is difficult to precisely draw the numerical comparison of term counts between orthologous genes annotated with redundant terms. Instead of the description only, GOOD further provides the GO graphs to reveal hierarchical-like relationships among divergent functionalities. Therefore, the redundancy of GO terms can be examined, and the context among compared terms is more comprehensive. In sum, GOOD can improve the interpretation in the molecular function from experiments in the model organism and provide clear comparative genomic annotation across organisms.
机译：完整基因组序列的积累增加了对功能注释的需求。关联直系同源物的现有功能注释可以加快注释过程，甚至可以检查现有注释。然而，当前基于蛋白质序列的直向同源物数据库在真核生物中提供了模棱两可和不完整的正交学。这是因为通过替代剪接（AS）衍生的同工型通常共享更高的序列相似性，以干扰基于序列的识别。面向基因的直系同源数据库（GOOD）在进行直系同源物描述之前，采用转录本的基因组位置来聚类AS衍生的同工型，以消除AS的干扰。从面向基因的表现形式，可以将同工型与其基因明确关联，以提供全面的直系同源信息，并进一步与旁系同源物区分开。除此以外，在直系同源基因之间显示同工型簇可以在转录水平上呈现进化变异。基于正交学，GOOD还包括来自基因本体论（GO）数据库的功能注释。但是，GO数据库中存在冗余的批注，将父项和子项都分配给同一基因。很难精确地标出用冗余术语注释的直系同源基因之间的术语计数的数值比较。除了描述以外，GOOD还提供了GO图以揭示不同功能之间的分层式关系。因此，可以检查GO项的冗余性，并且比较项之间的上下文更加全面。总之，GOOD可以改善模型生物实验中分子功能的解释，并为整个生物提供清晰的比较基因组注释。

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